Nucleic Acids Research Advance Access originally published online on September 8, 2006
Nucleic Acids Research 2006 34(17):4677-4684; doi:10.1093/nar/gkl555
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Nucleic Acids Research, 2006, Vol. 34, No. 17 4677-4684
© 2006 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
Molecular Biology |
Twin gradients in APOBEC3 edited HIV-1 DNA reflect the dynamics of lentiviral replication
Unité de Rétrovirologie Moléculaire, CNRS URA1930 Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France 1 Unité de Génomique des Microorganismes Pathogènes Institut Pasteur, 28 rue du Dr Roux, 75724 Paris cedex 15, France
*To whom correspondence should be addressed. Tel: +33 1 45 68 83 65; Fax: +33 1 45 68 88 74; Email: simon{at}pasteur.fr
Received June 21, 2006. Revised July 17, 2006. Accepted July 17, 2006.
The human immunodeficiency virus (HIV) Vif protein blocks incorporation of two host cell cytidine deaminases, APOBEC3F and 3G, into the budding virion. Not surprisingly, on a vif background nascent minus strand DNA can be extensively edited leaving multiple uracil residues. Editing occurs preferentially in the context of TC (GA on the plus strand) and CC (GG) depending on the enzyme. To explore the distribution of APOBEC3F and –3G editing across the genome, a product/substrate ratio (AA + AG)/(GA + GG) was computed for a series of 30 edited genomes present in the data bases. Two highly polarized gradients were noted each with maxima just 5' to the central polypurine tract (cPPT) and LTR proximal polypurine tract (3'PPT). The gradients are in remarkable agreement with the time the minus strand DNA remains single stranded. In vitro analyses of APOBEC3G deamination of nascent cDNA spanning the two PPTs showed no pronounced dependence on the PPT RNA:DNA heteroduplex ruling out the competing hypothesis of a PPT orientation effect. The degree of hypermutation varied smoothly among genomes indicating that the number of APOBEC3 molecules packaged varied considerably.
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors
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